X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FContactMapRenderer.java;h=9a295f98262d597ea7f6c86cca77e6c0f73e2899;hb=8b5ae15a094b5a90238bfe39ce10310ed92184d1;hp=e54f4714bc1c10e1f71a357b2882000480553a45;hpb=e122bcdde6d11fd3711eda525924d0d737a4f62a;p=jalview.git
diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index e54f471..9a295f9 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -1,11 +1,31 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
+import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Graphics;
-import java.util.Iterator;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Stroke;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
@@ -25,6 +45,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
{
/**
* bean holding colours for shading
+ *
* @author jprocter
*
*/
@@ -34,10 +55,12 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
* shown when no data available from map
*/
Color no_data;
+
/**
* shown for region not currently visible - should normally not see this
*/
Color hidden;
+
/**
* linear shading scheme min/max
*/
@@ -48,6 +71,21 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
*/
Color selMinColor, selMaxColor;
+ /**
+ *
+ * @param no_data
+ * - colour when no data available
+ * @param hidden
+ * - colour if this row is hidden
+ * @param maxColor
+ * - colour for maximum value of contact
+ * @param minColor
+ * - colour for minimum value of contact
+ * @param selMinColor
+ * - min colour if the contact has been selected
+ * @param selMaxColor
+ * - max colour if contact is selected
+ */
public Shading(Color no_data, Color hidden, Color maxColor,
Color minColor, Color selMinColor, Color selMaxColor)
{
@@ -66,6 +104,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
/**
* build an EBI-AlphaFold style renderer of PAE matrices
+ *
* @return
*/
public static ContactMapRenderer newPAERenderer()
@@ -77,8 +116,8 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
{
return new Shading(Color.pink, Color.red,
- new Color(246, 252, 243), new Color(0, 60, 26),
- new Color(26, 0, 60), new Color(243, 246, 252));
+ new Color(247, 252, 245), new Color(0, 68, 28),
+ new Color(28, 0, 68), new Color(245, 247, 252));
}
};
}
@@ -99,7 +138,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
boolean hasHiddenColumns, AlignViewportI viewport,
HiddenColumns hiddenColumns, ColumnSelection columnSelection,
AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
- int eRes, float min, float max, int y)
+ int eRes, float min, float max, int y, boolean isVectorRendering)
{
if (sRes > aa_annotations.length)
{
@@ -107,15 +146,25 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
}
eRes = Math.min(eRes, aa_annotations.length);
- int x = 0, y2 = y;
+ int x = 0, topY = y;
- g.setColor(shade.no_data);
-
- g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
+ // uncomment below to render whole area of matrix as pink
+ // g.setColor(shade.no_data);
+ // g.fillRect(x, topY-_aa.height, (eRes - sRes) * charWidth,
+ // _aa.graphHeight);
+ boolean showGroups = _aa.isShowGroupsForContactMatrix();
int column;
int aaMax = aa_annotations.length - 1;
ContactMatrixI cm = viewport.getContactMatrix(_aa);
+ if (cm == null)
+ {
+ return;
+ }
+ Graphics2D g2d = (Graphics2D) g;
+ g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_OFF);
+ g2d.setStroke(thinRectangularLineStroke);
while (x < eRes - sRes)
{
column = sRes + x;
@@ -146,52 +195,38 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
x++;
continue;
}
- Color gpcol = (cm==null) ? Color.white: cm.getColourForGroup(cm.getGroupsFor(column));
+ // ContactListI from viewport can map column -> group
+ Color gpcol = (cm == null) ? Color.white
+ : contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column));
// feature still in development - highlight or omit regions hidden in
// the alignment - currently marks them as red rows
boolean maskHiddenCols = false;
- // TODO: pass visible column mask to the ContactGeometry object so it maps
+ // TODO: optionally pass visible column mask to the ContactGeometry object
+ // so it maps
// only visible contacts to geometry
// Bean holding mapping from contact list to pixels
+ // TODO: allow bracketing/limiting of range on contacts to render (like
+ // visible column mask but more flexible?)
+
+ // COntactListI provides mapping for column -> cm-groupmapping
final ContactGeometry cgeom = new ContactGeometry(contacts,
_aa.graphHeight);
- for (int ht = y2, eht = y2
- - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
+ for (int ht = 0, botY = topY
+ - _aa.height; ht < _aa.graphHeight; ht += cgeom.pixels_step)
{
- ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht,
- y2 - ht + cgeom.pixels_step);
+ ContactGeometry.contactInterval ci = cgeom.mapFor(ht);
// cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
// cend = (int) Math.min(contact_height,
// Math.ceil(cstart + contacts_per_pixel * pixels_step));
Color col;
- boolean rowsel = false, containsHidden = false;
+ boolean rowsel = false;
+ boolean containsHidden = false;
if (columnSelection != null)
{
- if (_aa.sequenceRef == null)
- {
- rowsel = columnSelection.intersects(ci.cStart, ci.cEnd);
- }
- else
- {
- // TODO check we have correctly mapped cstart to local sequence
- // numbering
- int s = _aa.sequenceRef.findIndex(ci.cStart);
- int e = _aa.sequenceRef.findIndex(ci.cEnd);
- if (maskHiddenCols && hasHiddenColumns)
- {
- // TODO: turn into function and create test !!
- Iterator viscont = hiddenColumns
- .getVisContigsIterator(s, e, false);
- containsHidden = !viscont.hasNext();
- }
- if (s > 0 && s < _aa.sequenceRef.getLength())
- {
- rowsel = columnSelection.intersects(s, e);
- }
-
- }
+ rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
+ maskHiddenCols);
}
// TODO: show selected region
if (colsel || rowsel)
@@ -216,21 +251,23 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
{
col = shade.hidden;
}
- if (gpcol!=null && gpcol!=Color.white) {
+ if (showGroups && gpcol != null && gpcol != Color.white)
+ {
// todo - could overlay group as a transparent rectangle ?
- col = new Color((int)(((float)(col.getRed()+gpcol.getRed()))/2f),
- (int)(((float)(col.getGreen()+gpcol.getGreen()))/2f),
- (int)(((float)(col.getBlue()+gpcol.getBlue()))/2f));
+ col = new Color((int) ((col.getRed() + gpcol.getRed()) / 2f),
+ (int) ((col.getGreen() + gpcol.getGreen()) / 2f),
+ (int) ((col.getBlue() + gpcol.getBlue()) / 2f));
}
g.setColor(col);
-
- if (cgeom.pixels_step > 1)
+ if (isVectorRendering || cgeom.pixels_step > 1)
{
- g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
+ g2d.fillRect(x * charWidth, botY + ht, charWidth,
+ cgeom.pixels_step);
}
else
{
- g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht);
+ g2d.drawLine(x * charWidth, botY + ht, (x + 1) * charWidth - 1,
+ botY + ht);
}
}
x++;
@@ -238,10 +275,13 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
}
+ private static Stroke thinRectangularLineStroke = new BasicStroke(1,
+ BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL);
+
Color shadeFor(float min, float max, float value)
{
- return jalview.util.ColorUtils.getGraduatedColour(value, 0, shade.minColor,
- max, shade.maxColor);
+ return jalview.util.ColorUtils.getGraduatedColour(value, 0,
+ shade.minColor, max, shade.maxColor);
}
public Color getColorForRange(float min, float max, ContactListI cl,
@@ -257,7 +297,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
{
ContactRange cr = cl.getRangeFor(i, j);
// average for moment - probably more interested in maxIntProj though
- return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(),
+ return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMin(),
0, shade.selMinColor, max, shade.selMaxColor);
}